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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

MarkDuplicates analysis of large wheat chromosomes



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    Genevieve Brandt (she/her)

    Hi John,

    Could you share your entire command, stack trace, and GATK version? We did have a somewhat similar issue come up with the wheat genome and MarkDuplicates but I don't have enough information about your case to know if there is a good workaround.



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    Miriam Marin Sanz

    Hi Genevieve,


    We have also the same problem with the durum wheat genome.

    Warning messages:

    WARNING 2023-02-23 09:22:48     BAMRecordCodec  Reference length is too large for BAM bin field.
    WARNING 2023-02-23 09:22:48     BAMRecordCodec  Reads on references longer than 536870912bp will have bin set to 0.


    The command was:

    gatk MarkDuplicates -I sample.sorted.bam -M sample_dedup_metrics.txt -O sample_sorted_dedup.bam

    GATK version:

    The Genome Analysis Toolkit (GATK) v4.3.0.0
    HTSJDK Version: 3.0.1
    Picard Version: 2.27.5


    Thank you in advance,


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